C-55 (Comprehensive Panel) Pathogenic Variant Detected€¦ · Capstone Diagnostics 8601 Dunwoody Place, Ste 444 Atlanta, GA 30350 844-497-8851 Laboratory Director:John Hanson, PhD

ISPM Labs DBACapstone Diagnostics8601 Dunwoody Place, Ste 444 Atlanta, GA 30350www.capstonediagnostics.com844-497-8851Laboratory Director:John Hanson, PhDCLIA Number: 11D2073885

TEST PERFORMED

C-55 (Comprehensive Panel)Targeted next-generation sequencing was performed on this specimen. See Methods and Limitations section formore information.

VARIANT SUMMARYVariants Detected Genotype Phenotype Assessment

c.3481_3491delGAAGATACTAG

BRCA1

p.E1161fs*3

Heterozygous Hereditary Breast And/orOvarian Cancer Pathogenic

VARIANT INTERPRETATION

p.E1161fs*3

c.3481_3491delGAAGATACTAG

Pathogenic

BRCA1 Interpretation: BRCA1 is a tumor suppressor responsible for repair of DNA double strandbreaks and maintenance of genomic stability [2]. Deletions, loss of heterozygosity, and loss-of-function mutations cause BRCA1 inactivation [6, 4].

RESULT

Pathogenic Variant Detected

PATIENT INFORMATION PROVIDER INFORMATION SPECIMEN

Patient Name: Michelle Davis

Date of Birth: May 5, 1970

Age: 48

Sex: Female

Ethnicity: Caucasian

Physician: Dr. E Smith

Client: General Hospital

Client ID: ABC123

Accession ID: CAP0129384

Specimen Type: BuccalCollection Date: Sep 13, 2018

Date Accessioned: Sep 14, 2018 Date Reported: Oct 5, 2018

Page 1 of 3Capstone Diagnostics | 8601 Dunwood Place | Building 400 | Suite 444 | Atlanta, GA | 30350

C-55 (Comprehensive Panel)

Accession ID: CAP0129384Laboratory Director: John Hanson, PhD CLIA Number: 11D2073885

GENES TESTEDAPC, ATM, AXIN1, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDC73, CDH1, CDKN1C, CDKN2A, CHEK2, DICER1, DIS3L2, EPCAM, FH, FLCN, GPC3, GREM1, MEN1, MET, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PRKAR1A, PALB2, PMS2, POLD1, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, REQL4, RET, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARC4A, STK11, SUFU, TP53, TSC1, TSC2, VHL, WT1

METHODS AND LIMITATIONSDNA extracted from patient’s saliva sample is quantified using Qubit 2.0 Fluorimeter (Life Technologies Inc.). Germline mutations of APC, ATM, AXIN1, BAP1, BARD1, BMPR1A, BRCA1, BRCA2, BRIP1, CDC73, CDH1, CDKN1C, CDKN2A, CHEK2, DICER1, DIS3L2, EPCAM, FH, FLCN, GPC3, GREM1, MEN1, MET, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PRKAR1A, PALB2, PMS2, POLD1, PTCH1, PTEN, RAD50, RAD51C, RAD51D, RB1, REQL4, RET, SDHA, SDHB, SDHC, SDHD, SMAD4, SMARC4A, STK11, SUFU, TP53, TSC1, TSC2, VHL, WT1 genes are tested by sequencing the entire coding region for each gene with 5 bp of padding at both ends. The panel consists of amplicons that cover 98% of all coding regions of the genes listed above. Each sample template is tagged with a unique barcode for sample identification before processing. Sequencing is performed on the Ion Torrent S5 (Life Technologies Inc.) using AmpliSeq and Ion Chef technologies, and Hi-Q View chemistry. Data obtained are analyzed using the Applied Biosystems Ion Torrent variant analyzing software, which includes signal processing, base calling,quality score assignment, adapter trimming, alignment to human genome 19 reference (hg19), coverage analysis, and variant calling. Variant annotation is performed on the QIAGEN Clinical Insight software. Sanger sequencing confirmation is performed on all pathogenic, likely pathogenic, and variant of unknown significance samples through Eurofins Clinical Molecular Testing Services, LLC.

Based on validation studies, our method has a >95% sensitivity and specificity for detecting single nucleotide variants, insertions/deletions, and other frame shift mutations. However, some rare and novel genetic variations might not be detected by this method. Genes other then those listed above that are associated with certain types of cancer are beyond the scope of this test.

QIAGEN Clinical Insight (QCITM) is a variant analysis, interpretation and decision support tool for research and clinical labs analyzing human genetics data and is not intended to be used for diagnostic purposes. QCI Interpret software includes the following underlying databases, data reference sets and tools; QIAGEN Clinical Insight-Interpret (5.3.20180727), Ingenuity Knowledge Base (Rohan 180914.001), CADD (v1.3), Allele Frequency Community (2018-05-25), EVS (ESP6500SI-V2), JASPAR (2013-11), Ingenuity Knowledge Base Snapshot Timestamp (2018-09-14 07:13:41.0), Vista Enhancer hg18 (2012-07), Vista Enhancer hg19 (2012-07), Clinical Trials (Rohan 180914.001), PolyPhen-2 (v2.2.2), 1000 Genome Frequency(phase3v5b), ExAC (0.3.1), iva (Jun 26 11:55 iva-1.0.476233.jar), PhyloP hg18 (2009-11), PhyloP hg19 (2009-11), DbSNP(151), TargetScan (6.2), CentoMD (4.2), OMIM (May 26, 2017), gnomAD (2.0.1), BSIFT (2016-02-23), TCGA (2013-09-05), Clinvar (2018-04-06), DGV (2016-05-15), COSMIC (v84), HGMD (2018.1), SIFT4G (2016-02-23)

DISCLAIMERFalse positives and false negatives are possible. Such errors can be due to contamination, technical errors, andinterference from rare genetic variants. It is recommended to consider alternative methods before taking any clinicalaction. Consulting your results with a genetic counselor is highly recommended. This test was developed, and itsperformance characteristics determined by Capstone Diagnostics. The laboratory is regulated and accredited by CLIAand the Joint Commission (JCHO) as qualified to perform high-complexity testing. This test is used for clinicalpurposes. It should not be regarded as investigational or for research.

Page 2 of 3Capstone Diagnostics | 8601 Dunwood Place | Building 400 | Suite 444 | Atlanta, GA | 30350

C-55 (Comprehensive Panel)

Accession ID: CAP0129384 Laboratory Director: John Hanson,PhD CLIA Number: 11D2073885

SELECTED CITATIONS

Caux-Moncoutier V, Castéra L, Tirapo C, Michaux D, Rémon MA, Laugé A, Rouleau E, De Pauw A, Buecher B, Gauthier-Villars M, Viovy JL, Stoppa-Lyonnet D, Houdayer C (2011) EMMA, a cost- and time-effective diagnostic method forsimultaneous detection of point mutations and large-scale genomic rearrangements: application to BRCA1 and BRCA2 in1,525 patients. Hum Mutat. 2011 Mar;32(3):325-34. Epub 2011 Feb 8 (PMID: 21120943)

1.

Farmer H, McCabe N, Lord CJ, Tutt AN, Johnson DA, Richardson TB, Santarosa M, Dillon KJ, Hickson I, Knights C, MartinNM, Jackson SP, Smith GC, Ashworth A (2005) Targeting the DNA repair defect in BRCA mutant cells as a therapeuticstrategy. Nature. 2005 Apr 14;434(7035):917-21 (PMID: 15829967)

2.

Spugnesi L, Gabriele M, Scarpitta R, Tancredi M, Maresca L, Gambino G, Collavoli A, Aretini P, Bertolini I, Salvadori B,Landucci E, Fontana A, Rossetti E, Roncella M, Naccarato GA, Caligo MA (2016) Germline mutations in DNA repair genesmay predict neoadjuvant therapy response in triple negative breast patients. Genes Chromosomes Cancer. 2016Dec;55(12):915-924. Epub 2016 Jul 26 (PMID: 27328445)

3.

Walsh T, Casadei S, Coats KH, Swisher E, Stray SM, Higgins J, Roach KC, Mandell J, Lee MK, Ciernikova S, Foretova L,Soucek P, King MC (2006) Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breastcancer. JAMA. 2006 Mar 22;295(12):1379-88 (PMID: 16551709)

4.

Walsh T, Casadei S, Lee MK, Pennil CC, Nord AS, Thornton AM, Roeb W, Agnew KJ, Stray SM, Wickramanayake A,Norquist B, Pennington KP, Garcia RL, King MC, Swisher EM (2011) Mutations in 12 genes for inherited ovarian, fallopiantube, and peritoneal carcinoma identified by massively parallel sequencing. Proc Natl Acad Sci U S A. 2011 Nov01;108(44):18032-7. Epub 2011 Oct 17 (PMID: 22006311)

5.

Wooster R, Bignell G, Lancaster J, Swift S, Seal S, Mangion J, Collins N, Gregory S, Gumbs C, Micklem G (1995)Identification of the breast cancer susceptibility gene BRCA2. Nature. 1995 Dec 21-28;378(6559):789-92 (PMID: 8524414)

6.

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